rs7134375

Variant names:

• chr12-20320824-C-A
• rs7134375
• XR_931419.3:n.154G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-20320824-C-A
• chr12-20320824-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_931419.3(LOC105369688):​n.154G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,726 control chromosomes in the GnomAD database, including 11,952 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.39 (11952 hom., cov: 32)
• Consequence: LOC105369688 XR_931419.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

Genes affected

LOC105369688 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369688	XR_931419.3	n.154G>T		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59658 AN: 151608 Hom.: 11951 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.401

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.393 AC: 59695 AN: 151726 Hom.: 11952 Cov.: 32 AF XY: 0.390 AC XY: 28875 AN XY: 74104

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.395

Alfa AF: 0.422 Hom.: 29614

Bravo AF: 0.394

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.86

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7134375; hg19: chr12-20473758;